Root.R

#
# Copyright (C) 2013 EMBL - European Bioinformatics Institute
#
# This program is free software: you can redistribute it
# and/or modify it under the terms of the GNU General
# Public License as published by the Free Software
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# for more details.
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# can be used to endorse or promote products derived from
# this software without prior written permission. For
# written permission, please contact <sbotond@ebi.ac.uk>.

# Products derived from this software may not be called
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# Construct an alphabet containing integers representing a genomic region.
# Orientation is encoded in the sign.
.construct.alphabet<-function(root.size){
    symbols <- c(seq(-root.size,-1),seq(1,root.size))
    a       <- Alphabet()
    a$.symbols <- symbols
    a$.symbolLength <- root.size
    return(a)
}

# Construct a root sequence by asigning the "region alphabet" to the sites.
# The initial states correspond to the series of integers representing the genomic regions.
.construct.root<-function(root.size){
    alphabet = .construct.alphabet(root.size) 
    seq      = Sequence(length=root.size, alphabets=list(alphabet))
    setStates(seq,seq(1,root.size))
    return(list(seq=seq, alphabet=alphabet))
}